Variant report

Variant	rs360802
Chromosome Location	chr2:62936961-62936962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:62936577..62938663-chr2:62945664..62948457,3	K562	blood:
2	chr2:62936577..62938224-chr2:62946603..62948457,2	K562	blood:
3	chr2:62936543..62938335-chr2:62950956..62952981,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10208675	1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[ASN][1000 genomes]
rs1038570	0.89[CHD][hapmap]
rs11900596	0.87[ASN][1000 genomes]
rs12617178	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs13003895	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13030015	1.00[ASW][hapmap];0.81[GIH][hapmap];1.00[YRI][hapmap]
rs13398408	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1362311	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs1386400	0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs181723	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2054835	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2539979	0.89[ASN][1000 genomes]
rs2539986	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs2710635	0.84[ASN][1000 genomes]
rs2901518	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2931488	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2969300	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34503992	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs35499742	1.00[ASW][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36009942	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs360786	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360787	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360788	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360789	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360790	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360793	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs360794	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360795	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360796	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360798	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360805	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360806	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36193012	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4671049	0.81[ASN][1000 genomes]
rs6745862	0.83[ASN][1000 genomes]
rs6758263	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6760804	0.82[CHD][hapmap];0.94[GIH][hapmap];0.87[ASN][1000 genomes]
rs67657712	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7590973	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs360802	OTX1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62931800-62938000	Active TSS	Stomach Smooth Muscle	stomach
2	chr2:62933800-62938400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:62934200-62937400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr2:62934200-62945800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr2:62934200-62957800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:62934200-62957800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:62934400-62937200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr2:62934400-62938400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:62934400-62939800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:62934400-62957800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr2:62934600-62937200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr2:62934600-62937600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:62934600-62940600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:62934600-62942200	Weak transcription	Spleen	Spleen
15	chr2:62934600-62943800	Weak transcription	Aorta	Aorta
16	chr2:62934600-62945000	Weak transcription	Right Ventricle	heart
17	chr2:62934600-62945400	Weak transcription	Fetal Thymus	thymus
18	chr2:62934600-62947400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr2:62934600-62951600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:62934600-62951800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:62934600-62951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:62934600-62951800	Weak transcription	Esophagus	oesophagus
23	chr2:62934600-62951800	Weak transcription	Left Ventricle	heart
24	chr2:62934600-62952400	Weak transcription	Gastric	stomach
25	chr2:62934600-62957800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:62934600-62957800	Weak transcription	Thymus	Thymus
27	chr2:62934600-62957800	Weak transcription	HSMMtube	muscle
28	chr2:62934800-62938600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:62934800-62938800	Weak transcription	Fetal Kidney	kidney
30	chr2:62934800-62939200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:62934800-62939600	Strong transcription	HSMM	muscle
32	chr2:62934800-62951800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:62935000-62937000	Weak transcription	Primary B cells from cord blood	blood
34	chr2:62935000-62937400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr2:62935000-62948400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:62935200-62939000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:62935200-62943200	Weak transcription	HUVEC	blood vessel
38	chr2:62935200-62949000	Weak transcription	Fetal Intestine Large	intestine
39	chr2:62935400-62937000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:62935400-62937000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:62935400-62937000	Transcr. at gene 5' and 3'	Dnd41	blood
42	chr2:62935400-62937200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:62935400-62937400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:62935400-62939400	ZNF genes & repeats	NHLF	lung
45	chr2:62935600-62937200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:62935600-62939400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:62935600-62939800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:62935600-62940000	ZNF genes & repeats	GM12878-XiMat	blood
49	chr2:62935600-62941200	ZNF genes & repeats	NHDF-Ad	bronchial
50	chr2:62935600-62943400	Strong transcription	Primary hematopoietic stem cells	blood

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